High throughput screening of populations carrying naturally occurring mutations

ABSTRACT

Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Continuation application of U.S. patentapplication Ser. No. 15/961,542, filed Apr. 24, 2018, which is aContinuation application of U.S. patent application Ser. No. 15/674,126,filed Aug. 10, 2017, which is a Continuation application of U.S. patentapplication Ser. No. 15/434,801, filed Feb. 16, 2017, now U.S. Pat. No.9,745,627, which is a Continuation application of U.S. patentapplication Ser. No. 15/165,921, filed May 26, 2016, now U.S. Pat. No.9,574,230, which is a Continuation application of U.S. patentapplication Ser. No. 13/972,152, filed Aug. 21, 2013, now U.S. Pat. No.9,376,719, which is a Continuation application of U.S. patentapplication Ser. No. 13/447,871, filed Apr. 16, 2012, now U.S. Pat. No.8,614,073, which is a Continuation of U.S. patent application Ser. No.12/088,794, filed Sep. 8, 2008, which is the U.S. National Phase ofInternational Patent Application No. PCT/NL2006/000467, filed Sep. 21,2006, published on Apr. 5, 2007 as WO 2007/037678 A2, which claimspriority to U.S. Provisional Patent Application No. 60/721,528, filedSep. 29, 2005. The contents of these applications are hereinincorporated by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-WEB and is hereby incorporated byreference in its entirety. Said ASCII copy, created on April 24, 2018,is named 085342-1106SequenceListing.txt and is 12 KB.

BACKGROUND OF THE INVENTION Field of the Invention

The present invention, in the fields of molecular biology and geneticsrelates to improved strategies for identifying mutations in populations,based on the use of high throughput sequencing technologies. Theinvention further provides for kits that can be applied in the methods.

Description of the Background Art

Populations carrying mutations, either induced or naturally occurringare used in modern genomics research to identify genes affecting traitsof importance by reverse genetics approaches. This is in particularapplicable for plants and crops of agronomic importance, but suchpopulations are also useful, for other organisms such as yeast, bacteriaetc. Other organisms, such as animals, birds, mammals etc can also beused, but these populations are typically more cumbersome to obtain orto control. Nevertheless, it is observed that the invention describedherein is of a very general nature, and can be applied also to suchorganisms.

Mutagenized populations represent complementary tools for genediscovery, as such populations are commonly used to screen known genesfor loss-of-function mutations or assessing phenotype changes inorganisms with the mutated gene. The rate-limiting step is the screeningwork associated with identification of, respectively, organisms carryinga mutation in the gene of interest. Below, the principles of suchpopulations and the screening methods are described in more detail andmore efficient screening methods are presented which increase the valueof these tools for gene-discovery.

A technology that uses mutagenized populations is known as TILLING(Targeted Induced Local Lesions In Genomes) (McCallum et al., Nat.Biotechnol 2000, 18, 455-457, McCallum et al., Plant Physiology, 2000,123, 439-442; Till et al. Genome Research 2003, 13, 524-530) relies onrandom introduction of large numbers of mutations (mostly nucleotidesubstitutions) into the genome by treatment with ethyl methane sulfonate(EMS) or by ionizing radiation (fast neutron bombardment,) (Li et al,The Plant Journal, 2001, 27, 235-42). Every plant in the populationcarries several hundred (or thousand) mutations, some of which affectnormal development, morphology or otherwise confer a phenotype due toloss-of-function (knock-out, knock-down) of one or multiple genes ortheir regulatory sequences. A TILLING population generally contains asufficient number of plants to cover all genes with multiple independentmutations (5-20 per gene). A mutagenized plant population used inTILLING therefore usually consist of 3000-10,000 plants and can be usedin two ways:

Reverse Genetics

“Reverse Genetics” is the most common way of using TILLING populations.A gene of interest is identified, e.g., by transcript profiling or acandidate gene approach, and the question to be answered is whether thisgene affects a particular phenotypic trait of interest. The challengetherefore is to identify one (or several) plants with loss-of-functionmutations in this gene. This is commonly performed in a multi-stepscreening process, typically comprising the following steps:

-   -   1. Genomic DNA of a large number of (pooled) M2 plants        (e.g., 3072) of the TILLING population is isolated.    -   2. Pools of equal amounts of DNA from 8 to 32 plants per pool        are assembled, with the pooling level depending on the        sensitivity of the CEL I screening system (see below). This        results in a total of 96- to 384 pooled DNA samples in case of        3072 plants.    -   3. Labeled PCR primers are used to amplify parts of the gene        from all pooled DNAs. Overlapping PCR fragments are used to        cover the entire gene (e.g., 3*600 bp PCR fragments are        amplified from a 1500 bp gene).    -   4. Heteroduplexes of the PCR products obtained from the pooled        DNA samples are prepared and incubated with CEL I or another        enzyme which recognizes and cuts single nucleotide sequence        mismatches (e.g., mung bean nuclease, Si nuclease, Surveyor        etc.) and the treated samples are resolved on a denaturing        (sequencing) gel or by capillary electrophoresis.    -   5. Pools containing a plant carrying a mutation in the gene are        identified by observing bands of digestion products resulting        from CEL I treatment.

To identify the plant carrying the mutation, PCRs are repeated onindividual DNAs of the plants in the positive pools, followed bybi-directional Sanger sequencing.

Plants harboring a mutation are grown and out-crossed to wild-type toestablish causal relationship between the mutation and the observedphenotype change.

The advantage of CEL I screening (steps 3-5 above) is that pre-screeningthe pooled samples saves costs over sequencing all plants individuallyby Sanger sequencing.

However, a limitation of CEL I screening is that not all identifiedmutations affect gene function (e.g., silent substitutions) and this isnot known until the PCR products of individual plants in a positive poolare sequenced. Nevertheless, the CEL I mediated screening method iscost-saving compared to sequencing PCR products of all plantsseparately.

Another limitation is that CEL I screening involves running gels andscoring, a relatively cumbersome process that requires confirmation ofmutations from the second strand as gel-patterns are not alwaysclear-cut.

A third disadvantage is that CEL I screening is relatively insensitiveto mutation detection at the termini of the PCR product which may leadto some mutations going undetected. Further disadvantages of CEL I arethat it has been found that the enzyme is extremely sensitive toreaction conditions such as salt concentrations. This makes that theenzyme can only be used in a limited number of buffers, therebyhampering the broad use of CEL I. Another practical disadvantageassociated with the application of CEL I is that the enzyme is notreliable in cutting all mismatched heteroduplexes.

Finally, CEL I screening is incapable of distinguishing missensemutations (which are the most prevalent) from non-sense mutations,causing a great deal of screening work carried out on positive poolswithout yielding interesting mutations.

Forward Genetics

Plants of the mutagenized population are grown and phenotyped for traitsof interest. Plants with an interesting phenotype are then crossed to awild-type plant to out-cross mutations that are not linked to thephenotype of interest. Finally, the mutated gene responsible for thephenotype of interest is identified by positional cloning (using geneticmarkers), analogous to mapping QTL in conventional genetic mappingpopulations (F2, RIL etc). Although theoretically possible, mutagenizedpopulations are not commonly used this way.

The present invention was made in part improve the existing strategiesfor screening of mutagenized populations. It is an object of theinvention to provide efficient methods for screening large populationsfor the presence of mutations and to improve efficient assessment of themutations for impact on gene function, i.e., to reduce the amount ofeffort expended on screening mutations that do not lead to altered genefunctions. The present methods were designed to avoid the use of the CELI enzyme or its equivalents.

SUMMARY OF THE INVENTION

The present inventors found that using high throughput sequencingstrategies, the above-mentioned goals were achieved and mutagenizedpopulations, such as TILLING populations, populations wherein mutationshave been introduced rising (synthetic) mutagenic or DNA damagingoligonucleotides or, i.e. by Targeted Nucleotide Exchange (TNE) or byRegion Targeted Mutagenesis (RTM), or populations that contain naturallyoccurring mutations such as Single nucleotide polymorphisms (SNPs),small insertions and deletions, and variations in microsatellite repeatnumber could be efficiently screened for the presence of mutations ofinterest.

Definitions

In the following description and examples, a number of terms are used.To provide a clear and consistent understanding of the specification andclaims, including the scope to be given such terms, the followingdefinitions are provided. Unless otherwise defined herein, all technicaland scientific terms used have the same meaning as commonly understoodby those of ordinary skill in the art to which this invention belongs.The disclosures of all publications, patent applications, patents andother references are incorporated by reference herein in their entirety.

“TILLING” or “Targeting induced local lesions in genomes” is a generalreverse genetic strategy providing an allelic series of induced (point)mutations by random chemical or physical mutagenesis in combination withPCR-based screening to identify point mutations in a region of interest.In TILLING screening, regions of interest are amplified by PCR.Heteroduplexes between wild-type fragments and fragments harboring aninduced mutation are formed by denaturing and reannealing PCR products.These heteroduplexes are cleaved by CEL I and cleaved products areresolved. Throughput can be increased by pooling. Following discovery ofPCR products harboring sequence differences in a pool, PCR productsincluded in the pool are commonly screened again by Sanger sequencing ofindividual PCR products, thereby identifying the mutant plant and theexact sequence difference in the mutated gene.

“Mutagenized Population” refers to a population of organisms (usuallyplants, but other organisms, including animals such as Drosophila andmice may be used to create a mutagenized populations; Schimenti et al.,1998, Genome Research 8:698-710) that have been subjected to mutagenesis(chemical or physical) to yield a library of mutants. TILLINGpopulations may vary widely in size, and for certain purposes, partialTILLING populations can be used that contain 90, 80 70, 60, 50, 40 30 oreven only 20% of the original population. As an alternative tomutagenized populations, populations can be used wherein the populationis not mutagenized but comprises sub-populations that contain naturallyoccurring mutations such as Single nucleotide polymorphisms (SNPs),small insertions and deletions, and variations in microsatellite repeatnumber. These populations are particularly advantageous when mutagenizedpopulations are not readily accessible (humans) or where already largegermplasms are available. See for instance Comai et al., The PlantJournal, 2004, 37, 778-786. Such a population can be used in combinationwith a ‘reference DNA’.

“Targeted Nucleotide Exchange” or “TNE”. Targeted nucleotide exchange(TNE) is a process by which a synthetic oligonucleotide, partiallycomplementary to a site in a chromosomal or an episomal gene directs thereversal of a single nucleotide at a specific site. TNE has beendescribed using a wide variety of oligonucleotides and targets. Some ofthe reported oligonucleotides are RNA/DNA chimeras, contain terminalmodifications to impart nuclease resistance.

“Region targeted mutagenesis” or “RTM”. Region targeted mutagenesis is aprocess by which double-strand breaks at a predefined target site in thegenomic DNA are artificially created, resulting in repair of the breakby one of various available cellular repair mechanisms, mostly leadingto mutations at the site of the break. Double-strand breaks may becreated by introduction into the cell nucleus of zinc-finger nucleases(e.g. see Lloyd et al., 2005), meganucleases such as I-Scel (Epinat etal., 2003), or triplex-forming oligonucleotides coupled to mutagenicchemical groups (Havre et al., 1993).

“Nucleic acid”: A nucleic acid, as used herein, may include any polymeror oligomer of nucleotides with pyrimidine and purine bases, preferablycytosine, thymine (or uracil), adenine and guanine, respectively (SeeLehninger, Principles of Biochemistry, at 793-800 (Worth Pub. 1982)which is herein incorporated by reference in its entirety for allpurposes). Any deoxyribonucleotide, ribonucleotide or peptide nucleicacid component, and any chemical variant thereof, such as those withmethylated, hydroxymethylated or glycosylated forms of these bases, andthe like, are included. The polymers or oligomers may be heterogeneousor homogeneous in composition, and may be isolated from naturallyoccurring sources or may be artificially or synthetically produced. Anucleic acid may be DNA or RNA, or a mixture thereof, and may existpermanently or transiently in single-stranded or double-stranded form,including homoduplexes, heteroduplexes, and hybrid states.

“Tagging” refers to the addition of a tag or label to a nucleic acid inorder to be able to distinguish it from a second or further nucleicacid. Tagging can be performed, for example, by the addition of asequence identifier during amplification by using tagged primers or byany other means known in the art. Such a sequence identifier can be aunique base sequence of varying but defined length uniquely used foridentifying a specific nucleic acid sample. Typical example are ZIPsequences. Using such a tag, the origin of a sample can be determinedupon further processing. In the case of combining processed productsoriginating from different nucleic acid samples, the different nucleicacid samples are generally identified using different tags.

“Tagged library” refers to a library of tagged nucleic acids.

“Sequencing” refers to determining the order of nucleotides (basesequences) in a nucleic acid sample, e.g., DNA or RNA.

“Aligning and alignment” mean the comparison of two or more nucleotidesequences based on the presence of short or long stretches of identicalor similar nucleotides. Several methods for alignment of nucleotidesequences are known in the art, as will be further explained below.Sometimes the terms “assembly” or “clustering” are used as synonyms.

“High-throughput screening” (HTS) is a method of scientificexperimentation especially relevant to the fields of biology andchemistry. Through a combination of modern robotics and otherspecialized laboratory hardware, HTS allows an investigator toeffectively screen large numbers of samples simultaneously (or virtuallysimultaneously).

“Primers” in general refers to DNA strands which can prime the synthesisof DNA. DNA polymerase cannot synthesize DNA de novo without primers: itcan only extend an existing DNA strand in a reaction in which thecomplementary strand is used as a template to direct the order ofnucleotides to be assembled. The synthetic oligonucleotide moleculeswhich are used in a polymerase chain reaction (PCR) are referred toherein as primers.

“Primers with increased affinity” are primers with modified nucleotidessuch as PNA or LNA, which increases their thermal stability and allowsfor allele-specific amplification based on single nucleotide sequencedifferences. In order to achieve this, one or several modifiednucleotides are often included, preferably at the 3′-end of the primer.

“DNA amplification” is typically used to denote the in vitro synthesisof double-stranded DNA molecules using PCR. It is noted that otheramplification methods exist and they may also be used in the presentinvention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Schematic representation of clustered sequences resulting fromshotgun sequencing a gene to identify EMS-induced mutations. Mutationsare lighter, sequence errors darker colored. Sequence errors areexpected to be observed randomly and most often just once.

FIG. 2: Schematic representation of clustered tagged sequencingresulting from a 100 bp gene region amplified with 4 bp-tagged PCRprimers from a 3-D pooled library. Mutations are lighter, sequenceerrors darker colored. Plant IDs are known for mutations identified by 3tags (1,2,3) and (4,5,6) but not for those identified by less than 2 tag(7,8). Sequence errors are expected to be observed randomly and justonce.

FIG. 3: Illustration of the system of long and short PCR primers to usein tagging the sequences.

FIG. 4. Agarose gel estimation of the PCR amplification yield of eIF4Eexon 1 amplification for each of the 28 3D pools.

DETAILED DESCRIPTION OF THE INVENTION

In one aspect the invention is directed to a method for the detection ofa mutation in a target sequence in a member of a mutagenized populationcomprising the steps of:

-   (a) Isolating genomic DNA of each member of the mutagenized    population to provide for DNA samples of each member in the    population;-   (b) pooling the DNA obtained in step (a);-   (c) amplifying the target sequence with a pair of (optionally    labeled) primers from the DNA pools;-   (d) pooling the amplification products of step (c) to create a    library of amplification products;-   (e) optionally, fragmenting the amplification products in the    library;-   (f) determining the nucleotide sequence of the products and/or    fragments using high throughput sequencing;-   (g) identifying mutations by clustering (aligning) the sequences of    the fragments;-   (h) screening the identified mutations for a modified function of    the target sequence;-   (i) designing a primer directed to hybridize to the identified    mutation;-   (j) amplifying the library of step (d) with the primer of step (i)    and one of the primers of step (c);-   (k) identifying the member(s) carrying the mutation;-   (l) optionally, confirming the mutation by amplifying the target    sequence from the member(s) of step (k) using the primers of    step (c) and determining the sequence of the amplified product.

The isolation of DNA is generally achieved using common methods in theart such as the collection of tissue from a member of the population,DNA extraction (for instance using the Q-Biogene fast DNA kit),quantification and normalization to obtain equal amounts of DNA persample. As an example, the present invention is illustrated based on aTILLING population of 3072 plants and a gene of 1500 bp.

The pooling of the isolated DNA can for instance be achieved using a3-dimensional pooling scheme (Vandenbussche et al., 2003, The PlantCell, 15: 2680-93). The pooling is achieved preferably using equalamounts of DNA. The 3D-pooling scheme may comprise 15×15×14, resultingin 44 pools (15+15+14) containing 3072/14=219 or 3072/15=205 differentDNA samples per pool. Other pooling schemes can be used.

The pooling step typically serves to identify the plant containing anobserved mutation after one round of PCR screening. Pooling of the DNAfurther serves to normalize the DNAs prior to PCR amplification toprovide for a more equal representation in the libraries for sequencing.The additional advantage of the pooling of the DNA is that not allsequences have to be determined separately, but that the pools allow forrapid identification of the sequences of interest, in particular whentagged libraries are used. This facilitates the screening of large orcomplex populations in particular.

The amplification of the target sequence with a pair of optionallylabeled primers from the pools can be achieved by using a set of primersthat have been designed to amplify the gene of interest. As stated, theprimers may be labeled to visualize the amplification product of thegene of interest.

The amplification products are pooled, preferably in equal or normalizedamounts to thereby create a library of amplification products.Exemplary, the complexity of the library will be 3072 plants×1500 bygene sequence=4.6 Mb sequence.

The amplification products in the library may be randomly fragmentedprior to sequencing of the fragments in case the PCR product lengthexceeds the average length of the sequence traces. Fragmentation can beachieved by physical techniques, i.e., shearing, sonication or otherrandom fragmentation methods. In step (f), at least part, but preferablythe entire, nucleotides sequence of at least part of, but preferably ofall the fragments contained in the libraries is determined. In certainembodiments, the fragmentation step is optional. For instance, when theread length of the sequencing technique and the PCR fragments length areabout the same, there is no need for fragmentation. Also in the case oflarger PCR products this may not be necessary if it is acceptable thatonly part of the PCR product is sequenced for instance in case of 1500bp PCR product and read length of 400 (from each side) 700 bp remainunsequenced.

The sequencing may in principle be conducted by any means known in theart, such as the dideoxy chain termination method (Sanger sequencing),but this is less preferred given the large number of sequences that haveto be determined. It is however preferred and more advantageous that thesequencing is performed using high-throughput sequencing methods, suchas the methods disclosed in WO 03/004690, WO 03/054142, WO 2004/069849,WO 2004/070005, WO 2004/070007, and WO 2005/003375 (all in the name of454 Life Sciences), by Seo et al. (2004) Proc. Natl. Acad. Sci. USA101:5488-93, and technologies of Helios, Solexa, US Genomics, etcetera,which are herein incorporated by reference. It is most preferred thatsequencing is performed using the apparatus and/or method disclosed inWO 03/004690, WO 03/054142, WO 2004/069849, WO 2004/070005, WO2004/070007, and WO 2005/003375 (all in the name of 454 Life Sciences),which are herein incorporated by reference. The technology describedallows sequencing of 40 million bases in a single run and is 100 timesfaster and cheaper than competing technology. The sequencing technologyroughly consists of 5 steps: 1) fragmentation of DNA and ligation ofspecific adaptor to create a library of single-stranded DNA (ssDNA); 2)annealing of ssDNA to beads, emulsification of the beads in water-in-oilmicroreactors and performing emulsion PCR to amplify the individualssDNA molecules on beads; 3) selection of/enrichment for beadscontaining amplified ssDNA molecules on their surface 4) deposition ofDNA carrying beads in a PicoTiterPlate®; and 5) simultaneous sequencingin at least 100,000 wells by generation of a pyrophosphate light signal.The method will be explained in more detail below.

In a preferred embodiment, the sequencing comprises the steps of:

-   (a) annealing adapted fragments to beads, with a single adapted    fragment being annealed to each bead;-   (b) emulsifying the beads in water-in-oil microreactors, each    water-in-oil microreactor comprising a single bead;-   (c) loading the beads in wells, each well comprising a single bead;    and generating a pyrophosphate signal.

In the first step (a), sequencing adaptors are ligated to fragmentswithin the library. The sequencing adaptor includes at least a “key”region for annealing to a bead, a sequencing primer region and a PCRprimer region. Thus, adapted fragments are obtained.

In a second step, adapted fragments are annealed to beads, each beadannealing with a single adapted fragment. To the pool of adaptedfragments, beads are added in excess as to ensure annealing of onesingle adapted fragment per bead for the majority of the beads (Poissondistribution).

In a next step, the beads are emulsified in water-in-oil microreactors,each water-in-oil microreactor comprising a single bead. PCR reagentsare present in the water-in-oil microreactors allowing a PCR reaction totake place within the microreactors. Subsequently, the microreactors arebroken, and the beads comprising DNA (DNA positive beads) are enriched.

In a following step, the beads are loaded in wells, each well comprisinga single bead. The wells are preferably part of a PicoTiter™Plateallowing for simultaneous sequencing of a large amount of fragments.

After addition of enzyme-carrying beads, the sequence of the fragmentsis determined using pyrosequencing. In successive steps, thePicoTiter'Plate and the beads as well as the enzyme beads therein aresubjected to different deoxyribonucleotides in the presence ofconventional sequencing reagents, and upon incorporation of adeoxyribonucleotide a light signal is generated which is recorded.Incorporation of the correct nucleotide will generate a pyrosequencingsignal which can be detected.

Pyrosequencing itself is known in the art and described in e.g., WO03/004690, WO 03/054142, WO 2004/069849, WO 2004/070005, WO 2004/070007,and WO 2005/003375 (all in the name of 454 Life Sciences), which areherein incorporated by reference.

The mutations are identified by clustering of the sequenced fragments inthe amplified library. Identification of the mutations is achieved byaligning the determined sequences of the fragments of the libraries. Themajority of the sequences are wild-type (not mutated) but the inducedmutations and occasional sequencing errors are also observed. As theamplification libraries are sequenced with multifold redundancy(typically about 4- to 5-fold redundant), multiple observations of thesame sequence change is indicative of a mutation rather than asequencing error. See FIG. 1.

The clustering provides alignments of the fragments in the amplifiedlibrary. In this way for each PCR product in the library, a cluster isgenerated from sequenced fragments, i.e., a contig of the fragments, isbuild up from the alignment of the sequence of the various fragmentsobtained from the fragmenting in step (e).

Methods of alignment of sequences for comparison purposes are well knownin the art. Various programs and alignment algorithms are described in:Smith and Waterman (1981) Adv. Appl. Math. 2:482; Needleman and Wunsch(1970) J. Mol. Biol. 48:443; Pearson and Lipman (1988) Proc. Natl. Acad.Sci. USA 85:2444; Higgins and Sharp (1988) Gene 73:237-244; Higgins andSharp (1989) CABIOS 5:151-153; Corpet et al. (1988) Nucl. Acids Res.16:10881-90; Huang et al. (1992) Computer Appl. in the Biosci. 8:155-65;and Pearson et al. (1994) Meth. Mol. Biol. 24:307-31, which are hereinincorporated by reference. Altschul et al. (1994) Nature Genet. 6:119-29(herein incorporated by reference) present a detailed consideration ofsequence alignment methods and homology calculations.

The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al.,1990) is available from several sources, including the National Centerfor Biological Information (NCBI, Bethesda, Md.) and on the Internet,for use in connection with the sequence analysis programs blastp,blastn, blastx, tblastn and tblastx.

In the analysis of mutagenized populations, after the mutations havebeen identified, the identified mutations are assessed for a modifiedfunction of the associated gene, for instance the introduction of a stopcodon. This assessment is performed on the sequence itself, for exampleby six-frame translation. Once the interesting mutations have beenidentified, the mutations are further investigated to identify theassociated member of the population.

For each mutation that has been classified as an interesting mutation,an allele specific primer is designed that targets the mutation ofinterest. Thus, the allele specific primer is then used in combinationwith one of the primers used in the amplification of the pooled DNAsamples (either the reverse or the forward primer). One or both of theprimers may be labeled. The set of primers is used to amplify the poolsof DNA. The positive pools are identified and the mutant plant isidentified. In the above-mentioned 3D pooling scheme, the allelespecific PCR with the set of primers to screen the 3D pooled DNA sampleplates results in the identification of 3 positive pools (one in eachdimension), which specifies the library address of the mutant plant.

In certain embodiments, the allele-specific primers comprise alternativenucleotides such as Locked Nucleic Acids (LNA) or Peptide Nucleic Acids(PNA) to increase their specificity. Such nucleic acids are widely knownin the art and are commercially available from a choice of suppliers.

Confirmation of the mutation is achieved by amplification of the targetsequence from the identified mutant plant. This amplification isperformed with the primers from step (c). The nucleotide sequence of theamplified product is determined and by comparison with the consensussequence, the mutation is identified. The sequencing is preferablyperformed Sanger sequencing.

In one aspect the invention pertains to a method for the detection of amutation in a target sequence in a member of a mutagenized populationcomprising the steps of:

-   (a) isolating genomic DNA of each member of the mutagenized    population to provide DNA samples of each member in the population;-   (b) pooling the DNA obtained in step (a);-   (c) amplifying a part or segment of the target sequence with a pair    of tagged (optionally labeled) primers from the DNA pools,    preferably wherein at least one of the primers comprise a    gene-specific section, a tag and a sequence primer binding site;-   (d) pooling the amplification products of step (c) to create a    library of amplification products;-   (d) determining the nucleotide sequence of the amplification    products using high throughput sequencing;-   (f) identifying mutations by clustering (aligning) the sequences of    the fragments;-   (g) identifying the member(s) having the mutation using the tags;-   (h) optionally, confirming the mutation by amplifying the target    sequence from the member(s) of step (g) using the primers of    step (c) and determining the sequence of the amplified product.

The isolation of genomic DNA of the members of the mutagenizedpopulation and the pooling of the isolated DNA can be carried outessentially as described above.

A part or segment of the target sequence is amplified using a pair oftagged primers that may be labeled. Preferably, for each pool of eachdimension, a different primer is used. In the above illustration thismeans that 44 forward and 44 reverse primers are preferred. Preferably,each of the forward and reverse primers comprises

-   -   (i) a sequence primer binding site that can be used in the        following sequencing step,    -   (ii) a tag that serves to link the primer (and the resulting        amplification product) to the original member of the population,        and    -   (iii) a gene specific sequence that is capable of annealing to        the target sequence of interest (i.e., the gene).

In a typical embodiment the primer has the following order:

5′-Sequence primer binding site-Tag-Gene specific PCR primer sequence-3′The length of the sequence primer binding site and the gene specific PCRprimer sequence are those that are conventional in common PCR use, i.e.,independently from about 10 to about 30 bp with a preference for from 15to 25 bp. Preferably the part or segment of the sequence that isamplified corresponds to a length that can be sequenced in one run usingthe high throughput sequencing technologies described below. In certainembodiments the part or segment has a length of between about 50 bp toabout 500 bp, preferably from about 75 bp to about 300 bp and morepreferably between about 90 bp and about 250 bp. As stated above, thislength may vary with the sequencing technology employed including thoseyet to be developed.

By using primers (forward and/or reverse) containing a tag sequence thatis unique for each of the primers representing all pool dimensions, thespecific plant origin of each tag sequence is known as the sequenceprimer anneals upstream of the tag and as a consequence, the tagsequence is present in each amplification product. In certainembodiments, both forward and reverse primers are tagged. In otherembodiments, only on of the forward or reverse primers is tagged. Thechoice between one or two tags depends on the circumstances and dependson the read length of the high throughput sequencing reaction and/or thenecessity of independent validation. In the case of, e.g., a 100 bp PCRproduct that is sequenced unidirectionally, only one tag is needed. Inthe case of a 200 bp PCR product and a 100 bp read-length, doubletagging is useful in combination with bi-directional sequencing as itimproves efficiency 2-fold. It further provides the possibility ofindependent validation in the same step. When a 100 bp PCR product issequenced bi-directionally with two tagged primers, all traces,regardless of orientation, will provide information about the mutation.Hence both primers provide “address information” about which plantcontains which mutation.

The tag can be any number of nucleotides, but preferably contains 2, 3,4 or 5 nucleotides. With 4 nucleotides permuted, 256 tags are possible,whereas 3 nucleotides permuted provide 64 different tags. In theillustration used, the tags preferably differ by >1 base, so preferredtags are 4 by in length. Amplification using these primers results in alibrary of tagged amplification products.

In certain embodiments, a system of tags can be used wherein theamplification process includes

-   (1) a long PCR primer comprising (a) a 5′-constant section linked    to (b) a degenerate tag section (NNNN) linked to (c) a gene specific    section-3′ and-   (2) a short PCR primer in subsequent amplifications that consists    of (a) the 5′-contact section linked to (b) non-degenerate tag    section-3′ (i.e., a selection amongst NNNN).    The non-degenerate tag section can be unique for each sample, for    example, ACTG for sample 1, AATC for sample 2, etc. The short primer    anneals to a subset of the long primer. The constant section of the    primer can be used as a sequence primer. See FIG. 3.

The library preferably comprises equal, amounts of PCR products from allamplified pools. In the illustrative example, the library contains 3072plants×100 bp=307 kb sequence to be determined.

The PCR products in the library are subjected to a sequencing process asdisclosed above. In particular, the PCR products are attached to beadsusing the sequence primer binding site that corresponds to the sequencelinked to the bead. Thus the present embodiment does not requirefragmentation and adapter ligation. Rather, in this embodiment, theadapters have been introduced earlier via the PCR primer design. Thisimproves the reliability of the method. Following the annealing to thebeads, sequencing is performed as described above, i.e., (1)emulsification of the beads in water-in-oil microreactors, (2) emulsionPCR to amplify the individual ssDNA molecules on beads; (3) selectionof/enrichment for beads containing amplified ssDNA molecules on theirsurface, (4) transfer of the DNA carrying beads to a PicoTiterPlate®;and (5) simultaneous sequencing in 100,000 wells by a method thatgenerates a pyrophosphate light signal. Typical output is about200.000×100-200 by sequences, representing a 66 fold coverage of all PCRproducts in the library.

Clustering and alignment is performed essentially as described above.The individual plant containing the mutation can be identified using thetags. In the examples, the combination of the 3 tags denotes thepositive pools and the consequently the coordinates of the individualplant in the pools.

Confirmation of the mutation by re-sequencing of the PCR product of theidentified mutant sample is as described above.

Various pooling strategies can be used with the present invention,examples of which are multidimensional pooling (including 3D pooling) orcolumn-, row- or plate pooling.

High throughput sequencing methods that can be used here are described,for example, in Shendure et al., Science 309:1728-32. Examples includemicroelectrophoretic sequencing, hybridization sequencing/sequencing byhybridization (SBH), cyclic-array sequencing on amplified molecules,cyclic-array sequencing on single molecules, non-cyclical,single-molecule, real-time methods, such as, polymerase sequencing,exonuclease sequencing, or nanopore sequencing.

For optimal results, fragments or amplified products should be sequencedwith sufficient redundancy. Redundancy permits distinction between asequencing error and a genuine possible mutation. In certainembodiments, the redundancy of the sequencing is preferable at least 4,more preferably at least 5, but, as can be seen from the Examples,redundancies of more than 10, preferably more than 25 or even more than50 are considered advantageous, although not essential for thisinvention.

Advantages of the methods of the present invention reside inter alia inthe fact that mutations can be assessed in silico for their impact ongene function, meaning that a selection is made for the activemutations. Mutations conferring only silent substitutions can beselected against, thereby making the overall process more economical andefficient. This is a particular advantage with regard to the known CEL Ibased TILLING technology because the majority of CEL I mutations are C/Gto T/A transitions, of which only 5% commonly create stop codons(Colbert et al. 2001). The vast majority are missense mutations ofreduced interest. Efficient recognition of members in a population withstop codon mutations economizes the process and obviates the need foradditional screening of individual members of positive pools.

All mutations can be found with equal probability, irrespective of theirposition in the PCR product, in particular when the whole targetsequence is screened.

The method further avoids the use of CEL I digestion, heteroduplexformation and cumbersome gel scoring. The invention is thereforeinsensitive to pooling limitations associated with CEL I technology.

The invention further relates to kits that may contain one or morecompounds selected form the group consisting of: one or more (labeled)primers for a particular gene or trait, mutation- or allele-specificprimers. The kits may further contain beads, sequencing primers,software, descriptions for pooling strategies and other components thatare known for kits per se. In certain embodiments, kits are providedthat are dedicated to find specific mutations, for instancedisease-related mutations.

The invention is now illustrated here in below.

EXAMPLES

Screening a TILLING population can be advanced by using novelhigh-throughput sequencing methods, such as that of 454 Life Sciences(Margulies et al., 2005) or Polony Sequencing (Shendure et al., 2005).With the current state-of-the-art, 454 Life Sciences technology producesapproximately 20 Mb sequence in a single sequencing run. Read lengthsare approximately 100 bp per read. Assuming the screening of apopulation consisting of 3072 plants for mutations in a 1500 bp gene (asdescribed in the above-cited reference in Chapter 2), two approaches areenvisaged and described in more detail below.

-   (1) an approach where the entire 1500 bp gene is investigated for    the presence of EMS induced mutations; and-   (1) an approach where one or several 100 bp stretches are    investigated for the presence of EMS-induced mutations.

Example I Screening the Entire 1500 by Region

Genomic DNA of 3072 plants of the TILLING population is isolated. A 3-Dpooling scheme of equal amounts of DNA per plant is set up (e.g.,15×15×14), resulting in 44 pools (15+15+14=44) containing 3072/14=219 or3072/15=205 different DNA samples (Vandenbussche et al., supra).

This pooling step serves to permit identification of a plant containingan observed mutation after one round of PCR screening (step 8). Poolingof genomic DNAs further serves to normalize DNAs prior to PCRamplification to increase the probability that all DNAs are representedequally in the sequence library.

The 1500 bp gene is amplified from the pooled DNA samples using 1 pairof unlabelled PCR primers.

Equal amounts of PCR products from all pools wells are pooled to createa pooled PCR products library (complexity 3072 plants×1500 bp=4.6 Mbsequence).

The pooled PCR product library is subjected to shotgun sequencing usingconventional technologies (such as those provided by 454 Life Sciences)wherein PCR products are randomly fragmented, amplified on individualbeads and sequenced on the bead. Output is approximately 200,000 100 bpsequences, representing 4- to 5-fold coverage of all PCR products in thelibrary).

All sequences are clustered. The majority of sequences are wild-type butEMS-induced mutations (and sequence errors) are observed as well. SincePCR products are sequenced with 4-5 fold redundancy, multipleobservations of the same sequence change is indicative of a mutationrather than a sequencing error (FIG. 1).

Mutations are assessed for their impact on gene function such asintroduction of a stop-codon.

An allele-specific primer targeting a mutation of interest (with 3′Locked Nucleic Acid; LNA; or Peptide Nucleic Acid; PNA) is designed tobe used in combination with either the forward or reverse primer used instep 3 to screen the 3-D pooled DNA sample plate. Allele-specific PCRwill result in three positive pools (one of each dimension), whichspecifies the library address of the mutant plant.

The mutation is confirmed by amplifying the 1500 bp gene using theprimers of step 3, followed by (bi-directional) Sanger sequencing.

Example II Screening 100 bp Stretches (100 by is the Read Length of One454 Sequence Run)

Genomic DNA of 3072 plants of the TILLING population is isolated. A 3-Dpooling scheme of equal amounts of DNA per plant is set up (e.g.,15×15×14), resulting in 44 pools (15+15+14=44) containing 3072/14=219 or3072/15=205 different DNA samples (Vandenbussche et al., supra).

This pooling step serves to permit identification of the plantcontaining an observed mutation directly from the sequence data. Poolingof genomic DNAs further serves to normalize DNAs prior to PCRamplification to increase the probability that all DNAs are representedequally in the sequence library.

A 100 bp (or 200 bp) region of the gene is amplified from a the pools byPCR using tagged unlabelled PCR primers. This requires 44 forward and 44reverse primers (one for each pool of each dimension) with the followingconfiguration:

5′-Sequence primer binding site-4 bp Tag-Gene specific primersequence-3′.

By using tailed forward and reverse primers containing a 4 bp sequencetag that is different for each of the 44 primers representing all pooldimensions, the specific plant origin of each sequence is known as thesequence primer anneals upstream of the tag. Hence the tag sequence inpresent in each sequence trace. A 4 bp tag allows 4⁴=256 different tags.A 3 bp tag allows 64 different tag sequences—sufficient to distinguish44 tags—but tag sequences differing by more than 1 base are preferred.

Equal amounts of PCR products from all pools wells are pooled to createa pooled PCR products library (complexity 3072 plants×100 bp=307 kbsequence).

The pooled PCR product library is provided to 454 for sequencing, i.e.,PCR products are amplified and sequenced on the beads. Output isapproximately 200,000 100 bp sequences, representing 66-fold coverage ofall PCR products in the library.

All sequences (from either direction) are clustered; the majority ofsequences are wild-type sequences but EMS-induced mutations (andsequence errors) are observed as well. Since PCR products are sequencedwith 66 fold redundancy, multiple observations of the same sequencechange are indicative of a mutation rather than a sequencing error (FIG.1).

The coordinates of the individual plant containing the mutation will belmown immediately based on the unique combination of 3 tags sequencesthat occur in the sequence traces harboring the mutation (FIG. 2).

The mutation is confirmed by amplifying the 1500 bp gene using theprimers of step 3, followed by (bi-directional) Sanger sequencing.

Example III Identifying Specific Mutations in a Mutant Library of TomatoMutant Library of Tomato

This example describes the screening of a mutant library of tomato bymassive parallel sequencing in order to identify point mutations in aspecific locus (target gene). The mutant library used is an isogeniclibrary of inbred determinate tomato cultivar M82 consisting of 5075 M2families derived from EMS mutagenesis treatments. Seeds of each of the5075 M2 families were stored at 10% RH and 7° C. The origin andcharacteristics of the library are described in Menda et al. (Plant J.38: 861-872, 2004).

DNA Isolation

Leaf material was harvested from 5 individual greenhouse-grown plants ofeach of 3072 M2 families randomly chosen from the library. As anymutation occurring in the library will segregate in a Mendelian fashionin the M2 offspring, the pooling of the leaf material of 5 individual M2plants reduced the likelihood of overlooking any mutation as aconsequence of segregation to less than 0.1%. Genomic DNA was isolatedfrom the pooled leaf material using a modified CTAB procedure describedby Stuart and Via (Biotechniques, 14: 748-750, 1993). DNA samples werediluted to a concentration of 100 ng/μ1 in TE (10 mM Tris-HC1 pH 8.0, 1mM EDTA) and stored at −20° C. in 96-well microtitre plates.

3D Pooling of the DNA Samples

The isolated DNA samples were normalized to a concentration of 20 ng/μland subsequently pooled 4-fold resulting in 768 samples comprised ineight 96-well microtitre plates.Subsequently, these eight microtitre plates were subjected to a 3Dpooling strategy, resulting in 28 pools of DNA. The 3D pooling strategyconsisted of pooling together all DNAs in three different manners, thusensuring that each single 4-fold pool occurs only once in anX-coordinate pool, only once in a Y-coordinate pool and only once in aZ-coordinate pool. X-pools were assembled by pooling all DNA samplestogether per column of eight wells (e.g. AH-11) from all eightmicrotitre plates, resulting in 12 X-pools. Each X-pool therefore held 8(wells in a column)×8 (plates)=64 samples of 4-fold pools, representing256 M2 families. Y-pools were assembled by pooling all DNA samplestogether per row of twelve wells (e.g. A1-A12) from all eight microtitreplates, resulting in 8 Y-pools. Each Y-pool therefore held 12 (wells ina row)×8 (plates)=96 samples of 4-fold pools, representing 384 M2families. Z-pools were assembled by pooling all DNA samples togetherfrom an entire microtitre plate, resulting in 8 Z-pools. Each Z-pooltherefore held 12×8=96 samples of 4-fold pools, representing 384 M2families.

Target Locus

The target locus in this example was part of the tomato gene foreucaryotic initiation factor 4E (eIF4E). This gene has been shown to beinvolved in susceptibility to infection of potyviruses in Arabidopsis(Duprat et al., Plant J. 32: 927-934, 2002), lettuce (Nicaise et al.Plant Physiol. 132: 1272-1282, 2003) and Solanaceae (Ruffel et al.,Plant J. 32: 1067-1075, 2002; Mol.Gen.Genomics 274: 346-353, 2005), andspecific mutations in this gene are associated with recessive potyvirusresistance. The mutation screening described in this example was aimedto identify additional mutations in the tomato eIF4E gene as possiblesources of new potyvirus resistance. For the tomato eIF4E, only the cDNAsequence was known (NCBI accession numbers AY723733 and AY723734). Usinga PCR approach using primers designed on the basis of the cDNA sequence,fragments of the genomic sequence of the eIF4E locus of tomato cultivarMoneyberg were amplified and sequenced. This resulted in a sequence ofmost of the genomic locus of tomato eIF4E. The locus consists of 4 exonsand 3 introns. For the mutation screening, exon 1 of the gene was chosenas the target sequence (SEQ ID NO: 57).

SEQ ID NO: 57: Sequence of exon 1 of tomato Moneyberg eIF4E:ATGGCAGCAGCTGAAATGGAGAGAACGATGTCGTTTGATGCAGCTGAGAAGTTGAAGGCCGCCGATGGAGGAGGAGGAGAGGTAGACGATGAACTTGAAGAAGGTGAAATTGTTGAAGAATCAAATGATACGGCATCGTATTTAGGGAAAGAAATCACAGTGAAGCATCCATTGGAGCATTCATGGACTTTTTGGTTTGATAACCCTACCACTAAATCTCGACAAACTGCTTGGGGAAGCTCACTTCGAAATGTCTACACTTTCTCCACTGTTGAAAATTTTTGGGG

Primer Design for Target Locus Amplification

Primers were designed for the PCR amplification of exon 1 of tomatoeIF4E. The forward primers were designed to correspond to the ATG startcodon of the Open Reading Frame of exon 1, with 5′ of the ATG a tagsequence of four bases, providing a unique identifier for each of the 28pools. At the far 5′ end of the forward PCR primers, a 5′-C was added.All primers were phosphorylated at their 5′end to facilitate subsequentligation of adaptors. The sequence and names of the 28 forward primersare listed in Table 1. The tag sequences are underlined.

TABLE 1 Forward primers, sequences and pool identificationfor exon 1 amplification. 3D SEQ name sequence pool ID NO: 061009CACACATGGCAGCAGCTGAAATGG X1 SEQ ID NO: 1 061010 CACAGATGGCAGCAGCTGAAATGGX2 SEQ ID NO: 2 061011 CACGAATGGCAGCAGCTGAAATGG X3 SEQ ID NO: 3 061012CACGTATGGCAGCAGCTGAAATGG X4 SEQ ID NO: 4 061013 CACTCATGGCAGCAGCTGAAATGGX5 SEQ ID NO: 5 061014 CACTGATGGCAGCAGCTGAAATGG X6 SEQ ID NO: 6 061015CAGACATGGCAGCAGCTGAAATGG X7 SEQ ID NO: 7 061016 CAGAGATGGCAGCAOCTGAAATGGX8 SEQ ID NO: 8 061017 CAGCAATGGCAGCAGCTGAAATGG X9 SEQ ID NO: 9 061018CAGCTATGGCAGCAGCTGAAATGG X10 SEQ ID NO: 10 061019CAGTCATGGCAGCAGCTGAAATGG X11 SEQ ID NO: 11 061020CAGTGATGGCAGCAGCTGAAATGG X12 SEQ ID NO: 12 061021CATCGATGOCAGCAGCTGAAATGG Y1 SEQ ID NO: 13 061022CATGCATGGCAGCAGCTGAAATGG Y2 SEQ ID NO: 14 061023CTACGATGGCAGCAGCTGAAATGG Y3 SEQ ID NO: 15 061024CTAGCATGGCAGCAGCTGAAATGG Y4 SEQ ID NO: 16 061025CTCACATGGCAGCAGCTGAAATGG Y5 SEQ ID NO: 17 061026CTCAGATGGCAGCAGCTGAAATGG Y6 SEQ ID NO: 18 061027CTCGAATGGCAGCAGCTGAAATGG Y7 SEQ ID NO: 19 061028CTCGTATGGCAGCAGCTGAAATGG Y8 SEQ ID NO: 20 061029CTCTCATGGCAGCAGCTGAAATGG Z1 SEQ ID NO: 21 061030CTCTGATGGCAGCAGCTGAAATGG Z2 SEQ ID NO: 22 061031CTGACATGGCAGCAGCTGAAATGG Z3 SEQ ID NO: 23 061032CTGAGATGGCAGCAGCTGAAATGG Z4 SEQ ID NO: 24 061033CTGCAATGGCAGCAGCTGAAATGG Z5 SEQ ID NO: 25 061034CTGCTATGGCAGCAGCTGAAATGG Z6 SEQ ID NO: 26 061035CTGTCATGGCAGCAGCTGAAATGG Z7 SEQ ID NO: 27 061036CTGTGATGGCAGCAGCTGAAATGG Z8 SEQ ID NO: 28

The reverse primers were designed to correspond to basepair position 267to 287 of exon 1 in the non-coding strand. Again, 5′ of the priming partthe same series of tag sequences of four bases were included, providinga identifier for each of the 28 pools. At the far 5′ end of the reversePCR primers, a 5′-C was added. All primers were phosphorylated at their5′ end to facilitate subsequent ligation of adaptors. The sequence andnames of the 28 reverse primers are listed in Table 2. The tags areunderlined.

TABLE 2 Reverse primers sequences and pool identificationfor exon 1 amplification. 3D name sequence pool SEQ ID NO: 061037CACACCCCCAAAAATTTTCAACAGTG X1 SEQ ID NO: 29 061038CACAGCCCCAAAAATTTTCAACAGTG X2 SEQ ID NO: 30 061039CACGACCCCAAAAATTTTCAACAGTG X3 SEQ ID NO: 31 061040CACGTCCCCAAAAATTTTCAACAGTG X4 SEQ ID NO: 32 061041CACTCCCCCAAAAATTTTCAACAGTG X5 SEQ ID NO: 33 061042CACTGCCCCAAAAATTTTCAACAGTG X6 SEQ ID NO: 34 061043CAGACCCCCAAAAATTTTCAACAGTG X7 SEQ ID NO: 35 061044CAGAGCCCCAAAAATTTTCAACAGTG X8 SEQ ID NO: 36 061045CAGCACCCCAAAAATTTTCAACAGTG X9 SEQ ID NO: 37 061046CAGCTCCCCAAAAATTTTCAACAGTG X10 SEQ ID NO: 38 061047CAGTCCCCCAAAAATTTTCAACAGTG X11 SEQ ID NO: 39 061048CAGTGCCCCAAAAATTTTCAACAGTG X12 SEQ ID NO: 40 061049CATCGCCCCAAAAATTTTCAACAGTG Y1 SEQ ID NO: 41 061050CATGCCCCCAAAAATTTTCAACAGTG Y2 SEQ ID NO: 42 061051CTACGCCCCAAAAATTTTCAACAGTG Y3 SEQ ID NO: 43 061052CTAGCCCCCAAAAATTTTCAACAGTG Y4 SEQ ID NO: 44 061053CTCACCCCCAAAAATTTTCAACAGTG Y5 SEQ ID NO: 45 061054CTCAGCCCCAAAAATTTTCAACAGTG Y6 SEQ ID NO: 46 061055CTCGACCCCAAAAATTTTCAACAGTG Y7 SEQ ID NO: 47 061056CTCGTCCCCAAAAATTTTCAACAGTG Y8 SEQ ID NO: 48 061057CTCTCCCCCAAAAATTTTCAACAGTG Z1 SEQ ID NO: 49 061058CTCTGCCCCAAAAATTTTCAACAGTG Z2 SEQ ID NO: 50 061059CTGACCCCCAAAAATTTTCAACAGTG Z3 SEQ ID NO: 51 061060CTGAGCCCCAAAAATTTTCAACAGTG Z4 SEQ ID NO: 52 061061CTGCACCCCAAAAATTTTCAACAGTG Z5 SEQ ID NO: 53 061062CTGCTCCCCAAAAATTTTCAACAGTG Z6 SEQ ID NO: 54 061063CTGTCCCCCAAAAATTTTCAACAGTG Z7 SEQ ID NO: 55 061064CTGTGCCCCAAAAATTTTCAACAGTG Z8 SEQ ID NO: 56

Target Locus Amplification

The exon 1 of the target locus was amplified from the 3D pooled DNAsusing the forward and reverse primers described above. For each PCRreaction, a forward and a reverse primer were used with identical tags.For the amplification of exon 1 from each of the 28 3D pools, adifferent set of forward and reverse primers was used.The PCR amplification reaction conditions for each sample were asfollows:25 μl DNA (=50 ng); 5 μl RNase-mix ; 10 μ1 5x Herculase PCR-buffer; 0.6μ1 of the four dNTPs (20mM); 1.25 μ1 forward primer (50 ng/μ1); 1.25 μ1reverse primer (50 ng/μl); 0.5 μl Herculase DNA polymerase; 28.9 μlmilliQ-purified water. The RNase-mix consisted of 157.5 milliQ-purifiedwater+17.5 μl RNase.PCR amplifications were performed in a PE9600 thermocycler with a goldor silver block using the following conditions: 2 minutes hot-start of94° C., followed by 35 cycles of 30 sec at 94° C., 30 sec at 53° C., 1min at 72° C., and a final stationary temperature of 4° C. The PCRamplification efficiency was checked by analysis of 10 μl of PCRproducts on a 1% agarose gel. FIG. 4 shows the efficient amplificationof exon 1 PCR products from each of the 28 3D pools in comparison to aconcentration range of lambda DNA on the same gel.Following amplification, equal amounts of PCR products were mixed andpurified using the QIAquick PCR Purification Kit (QIAGEN), according tothe QIAquick® Spin handbook (page 18). On each column a maximum of 100μl of product was loaded. Products were eluted in 10 mM Tris-EDTA.

Sequence Library Preparation And High-Throughput Sequencing

Mixed amplification products from the 3D pools were subjected tohigh-throughput sequencing on a GS20 sequencer using 454 Life Sciencessequencing technology as described by Margulies et al. (Nature 437:376-380, 2005, and Online Supplements). Specifically, the PCR productswere ligated to adaptors to facilitate emulsion-PCR amplification andsubsequent fragment sequencing as described by Margulies et al. The 454adaptor sequences, emulsion PCR primers, sequence primers and sequencerun conditions were all as described by Margulies et al. The linearorder of functional elements in an emulsion-PCR fragment amplified onSepharose beads in the 454 sequencing process was as follows:454 PCR adaptor-454 sequence adaptor-C-nucleotide-4 by tag-targetamplification primer sequence 1-target fragment internal sequence-targetamplification primer sequence 2-4 by tag-G-nucleotide-454 sequenceadaptor-454 PCR adaptor-Sepharose bead.

454 Sequence Run Data-processing.

After base calling with 454 software for each region of the microtiterplate a file with FASTA formatted sequences was produced. These wereconcatenated into one file. Within this file a search was conducted witha regular expression to a 100% match of the forward primer preceded with5 nucleotides (C plus four by tag sequence). The same was done with thereverse primer extended with 5 nucleotides (C plus tag sequence). Allsequences were then grouped by their tag sequence (pool indentifiers) inseparate files. Each file was analysed with the ssahaSNP tool and theknown exon 1 nucleotide sequence as a reference. The ssahaSNP toolreported about all single nucleotide sequence differences and “indels”(single base insertions or deletions as a result of either mutagenesisor erroneous base-calling) of the 454 sequences versus the referencegenome. These single nucleotide sequence difference and indel statisticswere saved in a database and used for error rate analysis and pointmutation identification.

454 Sequencing Error Rate

The total number of correct sequences obtained from the data processingfor all 28 pools combined was 247,052. The sequences were divided in twogroups, those that aligned with the forward primer and coding strand (5′end) of the exon 1 PCR product (128,594=52%), and those that alignedwith the reverse primer and the complementary strand of the PCR product(118,458=48%). The number of sequences obtained from each of thedifferent pools and alignment groups ranged from 69 to 7269. On average,each of the 3072 M2 families should be represented 80 times in the totalcollection of sequences, and each allele 40 times. Within the alignmentgroup corresponding to the forward primer, 1338 sequences out of 128,594(1.2%) showed one or more single nucleotide sequence differences inrelation to the eIF4E reference sequence along a stretch of 63 bases ofaligned target sequence. For the reverse primer group, 743 sequences outof 118,458 (0.6%) showed one or more single nucleotide sequencedifferences in relation to the eIF4E reference sequence along a stretchof 102 bases of aligned target sequence. Therefore, the single basesubstitution error rate for both sequence groups combined equals 0.84%for a 165 base stretch, or 0.0051% per base position (0.5 errors per10,000 bases). This error rate is similar to the one reported byMargulies et al. of 0.004% for individual read substitution errors intest sequences, but much lower than for whole-genome resequencing(0.68%).A similar analysis of the occurrence of indels in both alignment groupsrevealed an indel incidence of 3883 (forward primer group) and 3829(reverse primer group) in a total of 247,052 sequences (is 3.1% in a 165by stretch). The indel occurrence rate therefore equals 0.01891% perbase position (1.89 indels per 10,000 bases). The indel rate issignificant higher than the base substitution error rate. Both types ofsequencing error combined occur on average at a frequency of 2.39 per10,000 bases, or 0.024 per base position. This error rate is much lowerthan reported by Margulies et al., and may be explained by the absenceof long homopolymer stretches in the eIF4e exon 1 sequence.

Detection of a Mutation in the Target Locus

Because the objective of this screen is the identification of(EMS)-induced point mutations (preferentially C→T and G→A mutations),all sequences representing indels in comparison to the referencesequence were discarded for the sake of the analysis in this example.Most of the single base substitutions occurred only once in any given 3Dpool, some occurred 2 or 3 times, or rarely more often. Since thesesingle base substitutions occur more or less uniformly at every positionof the aligned sequence, and at a more or less uniform frequency of0.005% per base, they were assumed to represent sequencing errors, andnot specific mutations that exist in the mutant library. However, at afew specific base positions in the scanned sequence, a much higherincidence of a specific single base sequence difference occurs. Suchsingle base sequence differences reveal mutations in the library, whenthe following criteria are fulfilled:

-   -   1. the single base sequence difference represents an C→T or G→A        mutation;    -   2. the incidence is higher than 20 per 10,000 sequence reads per        3D pool;    -   3. the single base sequence difference occurs in precisely one        and not more than one X-pool, Y-pool and Z-pool.        In this example, one such mutation was found in the alignment        group corresponding to the reverse primer, at base position 221        of the eIF4E exon 1 sequence. This mutation, a G→A mutation        (corresponding to C→T in the complementary strand) occured in        pool X12 at a frequency of 70 per 10,000 sequences, in pool Y3        at a frequency of 33 per 10,000 and in pool Z6 at 62 per 10,000        sequences. This same mutation at the same position did not occur        in any of the other pools, not even at background error rates.        The unique occurrence of this G221A mutation in only the three        pools allowed the identification of the original 4-fold pool of        DNA, representing four M2 families. DNA of each of these four M2        families was amplified individually with the primers 06F598 and        06F599 that are identical to the forward and reverse primers of        Tables 1 and 2, but without the 5′ five base sequence tags. The        amplified PCR products were subjected to conventional Sanger        sequencing. The sequence of the eIF4E gene in one of the four        families (coded “24”) revealed a dual peak at position 221,        corresponding to an overlapping G and A. This is indicative of        an M2 family pool, in which half the alleles are wild-type, and        the other half carry the G221A point mutation (FIG. 2). The        sequences of the other M2 families around base position 221 were        according to the reference (wild-type).        The mutation causes an arginine to glutamine substitution. Seeds        of this particular M2 family were planted in the greenhouse in        order to select for homozygous mutant individuals, that will be        used for phenotyping.        In a similar manner, two other point mutations were identified        in the 454 sequence reads. An estimation of the mutation density        of the M82 tomato mutant library therefore equals 3 mutations        per 165 by scanned sequence, or 18 mutations per 1000 bases in        3072 M2 families. This corresponds to mutation densities        reported for Arabidopsis (Greene et al., Genetics 164: 731-740,        2003).

REFERENCES

-   Colbert et al. 2001. High-throughput screening for induced point    mutations. Plant Physiology 126: 480-484.-   Duprat et al., 2002. The Arabidopsis eukaryotic initiation factor    (iso)4E is dispensable for plant growth but required for    susceptibility to potyviruses. Plant J. 32: 927-934.-   Epinat et al., 2003. A novel engineered meganuclease induces    homologous recombination in yeast and mammalian cells. Nucleic Acids    Research, 31(11): 2952-2962.-   Havre et al., 1993. Targeted mutagenesis of DNA using triple    helix-forming oligonucleotides linked to psoralen.    Proc.Natl.AcadSci. USA 90: 7879-7883.-   McCallum et al., 2000. Targeted screening for induced mutations.    Nature Biotechnology 18: 455-457.-   Greene et al., 2003. Spectrum of chemically induced mutations from a    large-scale reverse-genetic screen in Arabidopsis. Genetics 164:    731-740.-   Lloyd et al., 2005. Targeted mutagenesis using zinc-finger nucleases    in Arabidopsis. Proc.Natl.Acad.Sci. USA 102: 2232-2237.-   Margulies et al., 2005. Genome sequencing in microfabricated    high-density picolitre reactions. Nature 437: 376-380.-   Menda et al., 2004. In silico screening of a saturated mutation    library of tomato. Plant J. 38: 861-872.-   Nicaise et al., 2003. The eukaryotic translation initiation factor    4E controls lettuce susceptibility to the potyvirus lettuce mosaic    virusl. Plant Physiol. 132: 1272-1282.-   Ruffel et al., 2002. A natural recessive resistance gene against    potato virus Y in pepper corresponds to the eukaryotic initiation    factor 4E (eIF4E). Plant 32: 1067-1075. Ruffel et al., 2005. The    recessive potyvirus resistance gene pot-1 is the tomato orthologue    of the pepper pvr2-eIF4E gene. Mol. Gen. Genomics 274: 346-353.-   Shendure et al., 2005. Accurate multiplex polony sequencing of an    evolved bacterial genome. Scienceexpress Report, August 4.-   Stuart and Via, 1993. A rapid CTAB DNA isolation technique useful    for RAPD fingerprinting and other PCR applications. Biotechniques,    14: 748-750.-   Vandenbussche et al., 2003. Toward the analysis of the petunia MADS    box gene family by reverse and forward transposon insertion    mutagenesis approaches: B, C, and D floral organ identity functions    require SEPALLATA-like MADS box genes in petunia. The Plant Cell    15:2680-2693.

1. A method for detecting a mutation in one or more nucleic acidsamples, comprising: (a) providing a plurality of complexity reducedlibraries comprising amplified adapter-ligated nucleic acid fragments,wherein each nucleic acid fragment within a library comprises a sequencederived from a nucleic acid sample and one or more tag sequences fornucleic acid and/or sample identification; (b) pooling the plurality oflibraries of nucleic acid fragments; (c) performing high-throughputsequencing to sequence at least a portion of the pool of nucleic acidfragments, wherein the high-throughput sequencing is performed on asolid support and comprises annealing the nucleic acid fragments to thesolid support and amplifying the annealed nucleic acid fragments; and(d) aligning the sequences of the nucleic acid fragments and groupingthe sequences using the one or more tag sequences to identify a mutationand a nucleic acid and/or a sample comprising the mutation.
 2. Themethod according to claim 1, wherein the mutation is a single nucleotidepolymorphism.
 3. The method according to claim 1, wherein the mutationis a nucleotide insertion or deletion.
 4. The method according to claim1, wherein the mutation is a microsatellite repeat number variation. 5.The method according to claim 1, wherein the high-throughput sequencingis sequencing-by-synthesis.
 6. The method according to claim 1, whereinthe high-throughput sequencing is bi-directional sequencing.
 7. Themethod according to claim 1, wherein adapters are ligated to createlibraries of single-stranded DNA.
 8. The method according to claim 1,wherein the solid support comprises one or more beads.
 9. The methodaccording to claim 8, wherein step (c) comprises: (i) annealing thenucleic acid fragments to beads, each bead annealing with a singlenucleic acid fragment; (ii) emulsifying the beads in water-in-oilmicroreactors such that each microreactor contains a single bead; (iii)performing emulsion PCR to amplify nucleic acid fragments on the surfaceof the beads; (iv) selecting/enriching beads to which the amplifiednucleic acid fragments are attached; (v) placing the beads in wells suchthat each well comprises a single bead; and generating a pyrophosphatesignal.
 10. The method according to claim 1, wherein the nucleic acidfragments are sequenced with an average redundancy of at least
 10. 11.The method according to claim 1, wherein the nucleic acid fragments aresequenced with an average redundancy of at least
 25. 12. The methodaccording to claim 1, wherein the nucleic acid fragments are sequencedwith an average redundancy of at least
 50. 13. The method according toclaim 1, wherein step (d) comprises aligning the sequences of thenucleic acid fragments to a reference sequence or a consensus sequence.14. The method according to claim 1, wherein the nucleic acid fragmentsare each tagged at both ends.
 15. The method according to claim 1,wherein the nucleic acid fragments are each tagged with two differenttag sequences.
 16. The method according to claim 1, wherein the nucleicacid fragments each comprises a sequence derived from a nucleic acidsample flanked at both ends by tag sequences.
 17. The method accordingto claim 1, wherein the one or more tag sequences are for nucleic acididentification.
 18. The method according to claim 1, wherein the one ormore tag sequences are for sample identification.
 19. The methodaccording to claim 1, wherein the one or more tag sequences are fornucleic acid and sample identification.